New knowledge from small amounts of archived tissue samples

2021-09-30

Researchers at IGP have developed a novel method to study histone modifications in very small amounts of archived tissue samples. The method can be used to increase the knowledge about epigenetic alterations in cancer and other diseases and has been recently described in the journal Nucleic Acids Research.

Epigenetic DNA alterations means that there have been chemical modifications of the DNA without altering its sequence. A common epigenetic alteration is the modification of histones, i.e. the proteins that bind the DNA, which can result in activation or de-activation of genes.

To study histone modifications and gene regulation in different diseases researchers can use tissues that have been archived as paraffin-embedded samples. But the amount of clinical tissues of interest is limited and it is desirable to consume a minimal amount of paraffin-embedded samples in the analyses. With the method developed by the IGP researchers, the analyses can be performed with as little as 4 000 cells.

“Our method is called FACT-seq and it is the first highly sensitive method to efficiently profile the histone modifications in small amounts of paraffin-embedded tissue samples. The analyses could be applied to tissue sections that were only one hundredth of a millimeter thick,” says Xingqi Chen who has led the study which has involved several IGP research groups.

With FACT-seq the researchers could identify histone modifications that resulted in gene activation as well as those that de-activated genes. The method could also reveal disease-specific gene regulation in small amounts of archived human colorectal and human glioblastoma cancer tissue.

“We believe that FACT-seq can become a powerful tool for helping researchers to better understand epigenetic regulation in cancer and other human diseases,” says Xingqi Chen.

More information:
Paper in Nucleic Acids Research
Xingqi Chen’s research
Tobias Sjöblom’s research
Fredrik Swartling’s research
Lene Uhrbom’s research